The paper introduces the Semantic-Aware Subgraph State Space Model (SASG-SSM) for classifying whole slide images (WSIs) in histopathology. It groups spatially connected patches into semantic-aware subgraphs that preserve internal spatial organization, then uses a graph neural network encoder combined with a Mamba-based state space encoder to capture both local and global contextual information. Experiments on four WSI subtyping datasets show consistent performance gains over state‑of‑the‑art methods, with additional robustness in small‑cohort and few‑shot scenarios.
By Feixing Chen, Hao Lu, Lin Luo, Yan Xu
arXiv:2606. 02602v1 Announce Type: new Abstract: In computational pathology, Whole Slide Images (WSIs) survival analysis is crucial for patient prognosis assessment, but it faces multiple technical challenges.
By Yuanfang Chen, Peiqiang Yan, Yuntao Shou, Qian Zhao, Xiangyong Cao
arXiv:2609.00396v1 Announce Type: new
Abstract: Histopathological whole slide images (WSIs) are central to cancer diagnosis, but their gigapixel scale, tissue heterogeneity, weak slide-level supervis...
By Chad Wong, Sicheng Chen, Tianyi Zhang, Enhui Chai, Yueming Jin, Zeyu Liu, Fei Xia
The paper introduces an end‑to‑end framework for detecting and classifying cells in pathology images by jointly modeling visual features and instance‑level interactions. It employs a dynamic graph construction module that builds cell graphs from learnable queries and an instance‑aware graph network that filters and reorganizes features, integrating appearance and relational evidence. Experiments on multiple staining protocols show the method surpasses existing approaches in both detection and classification accuracy.
By Ruochen Liu, Yalin Zheng, Jingxin Liu, Jianfeng Zhang, Shoujun Huang, Dexing Kong, Haofeng Li, Wei Lou
arXiv:2511. 10260v2 Announce Type: replace-cross Abstract: Fine-Grained Visual Classification (FGVC) remains a challenging task due to subtle inter-class differences and large intra-class variations.
By Yongji Zhang, Siqi Li, Kuiyang Huang, Yue Gao, Yu Jiang
The paper introduces scalable Graph Transformers for classifying healthy versus tumor epithelial cells in whole-slide images of cutaneous squamous cell carcinoma. By constructing a full‑WSI cell graph and incorporating morphological, texture, and neighboring cell class features, the proposed SGFormer and DIFFormer models outperform traditional image‑based methods, achieving balanced accuracies above 85% on single‑WSI tests and 83.6% on multi‑WSI evaluations. The study demonstrates that preserving tissue‑level context through graph representations improves classification of morphologically similar cell types.
By Lucas Sanc\'er\'e, No\'emie Moreau, Katarzyna Bozek
Whole slide image (WSI) classification is an evidence-driven task, where diagnostic cues are often sparse, spatially organized, and class-dependent. Existing MIL and vision-language methods aggregate a large pool of patch features into a single global slide representation.
SCOUT is a concept‑grounded multimodal transformer that generates whole‑slide pathology reports by integrating local histological patterns, whole‑slide context, and expert‑curated diagnostic concepts. It uses evolving visual representations and recursively updated slide‑ and concept‑conditioned representations, with separate attention pathways during decoding that are fused adaptively for each token. Evaluated on TCGA‑BRCA, HistAI, and REG‑2025, SCOUT outperformed existing methods, improving BLEU, METEOR, and ROUGE‑L scores and raising the Clinical Report Quality Score on REG‑2025.
By Suryakant Singh, Saarthak Kapse, Joel Saltz, Prateek Prasanna
SpaFactor is a lightweight framework that predicts spatial gene expression from hematoxylin and eosin images by fusing central spot visuals with multiscale neighborhood context. It uses a residual MLP to map tissue microenvironment to low‑dimensional latent gene programs, which are decoded into coordinated multi‑gene predictions. Across five public cohorts, SpaFactor outperforms existing methods, especially for spatially variable genes, and better recovers biologically organized spatial patterns.
By Shiting Ruan, Xitong Ling, Qiming He, Ziyou Yan, Huaitian Yuan, Tian Guan, Ying Xiao, Xu Guan, Yonghong He
arXiv:2506. 11152v4 Announce Type: replace-cross Abstract: Single-cell transcriptomics and proteomics have become a great source for data-driven insights into biology, enabling the use of advanced deep learning methods to understand cellular heterogeneity and gene expression at the single-cell level.
By Hiren Madhu, Jo\~ao Felipe Rocha, Tinglin Huang, Siddharth Viswanath, Smita Krishnaswamy, Rex Ying
arXiv:2606.28676v2 Announce Type: replace-cross
Abstract: Predicting distant metastasis from the digital H & E slides of the primary tumor is a critical yet challenging task in computational patholog...
By Sandesh Pokhrel, Hamid Manoochehri, Beatrice S Knudsen, Tolga Tasdizen
arXiv:2607. 09104v1 Announce Type: cross Abstract: While the growing availability of image data has driven significant advances, labeling datasets remains costly and time-consuming.
By Camila Piscioneri Magalh\~aes, Lucas Pascotti Valem